A whole genome association analysis identifies loci associated with <i>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> infection status in US holstein cattle

<jats:title>Summary</jats:title><jats:p>The purpose of this study was to identify loci associated with <jats:italic>Mycobacterium avium</jats:italic> subspecies <jats:italic>paratuberculosis</jats:italic> (<jats:italic>Map</jats:italic>) infection status in US Holsteins using the <jats:italic>Illumina</jats:italic> BovineSNP50 BeadChip whole genome single nucleotide polymorphism (SNP) assay. Two hundred forty‐five cows from dairies in New York, Pennsylvania and Vermont enrolled in longitudinal herd studies between January 1999 and November 2007 were assessed for the presence of <jats:italic>Map</jats:italic> in both faecal and tissue samples. An animal was considered tissue infected if any sample contained at least one colony forming unit of <jats:italic>Map</jats:italic> per gram of tissue (CFU/g) and the same definition was employed for faecal samples. Each animal was genotyped with the <jats:italic>Illumina</jats:italic> BovineSNP50 BeadChip and after quality assurance filtering, 218 animals and 45 683 SNPs remained. We sought to identify loci associated with four different case/control classifications: presence of <jats:italic>Map</jats:italic> in the tissue, presence of <jats:italic>Map</jats:italic> in faeces, presence of <jats:italic>Map</jats:italic> in both tissue and faeces and presence of <jats:italic>Map</jats:italic> in tissue but not faeces. A case–control genome wide association study was conducted to test the four different classifications of <jats:italic>Map</jats:italic> infection status (cases) when compared with a <jats:italic>Map</jats:italic>‐negative control group (control). Regions on chromosomes 1, 5, 7, 8, 16, 21 and 23 were identified with moderate significance (<jats:italic>P</jats:italic> < 5 × 10<jats:sup>−5</jats:sup>). Two regions, one on chromosome 3 (near <jats:italic>EDN2</jats:italic>) and another on chromosome 9 (no positional gene candidates), were identified with a high level of association to the presence of <jats:italic>Map</jats:italic> in tissue and both tissue and faeces respectively (<jats:italic>P </jats:italic><<jats:italic> </jats:italic>5 × 10<jats:sup>−7</jats:sup>, genome‐wide Bonferonni <jats:italic>P </jats:italic><<jats:italic> </jats:italic>0.05).</jats:p>